[gmx-users] mdrun -rerun
Alex
nedomacho at gmail.com
Thu Jul 13 23:27:11 CEST 2017
And they are all exactly as they appear in my topology.
However, I think I found the solution:
https://www.researchgate.net/post/How_can_I_deal_with_this_error_in_gromacs_CNT_in_energygrp-excl_is_not_an_energy_group
Except I am not sure how to proceed. if I add:
energygrps = BUT DEC CBD
grompp throws this: "ERROR 1 [file prod_rerun.mdp]:
Energy group exclusions are not (yet) implemented for the Verlet scheme"
But the original simulation was performed with Verlet cutoff scheme. Do I
change that regardless of this fact?
Thanks,
Alex
On Thu, Jul 13, 2017 at 3:10 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Your input to gmx grompp -c is some other file though, and that's the set
> of index groups that matter, and the default ones should include those
> found by gmx make_ndx.
>
> Mark
>
> On Thu, Jul 13, 2017 at 11:06 PM Alex <nedomacho at gmail.com> wrote:
>
> > Same error in v. 2016.1.
> >
> > On Thu, Jul 13, 2017 at 2:39 PM, Alex <nedomacho at gmail.com> wrote:
> >
> > > Here you are, as run on the production tpr:
> > >
> > > $ gmx make_ndx -f prod.tpr
> > > GROMACS: gmx make_ndx, VERSION 5.0.5
> > >
> > > ........
> > > ........
> > >
> > > Reading structure file
> > > Reading file prod.tpr, VERSION 5.0.5 (single precision)
> > > Going to read 0 old index file(s)
> > > Analysing residue names:
> > > There are: 208 Other residues
> > > Analysing residues not classified as Protein/DNA/RNA/Water and
> splitting
> > > into groups...
> > >
> > > 0 System : 6537 atoms
> > > 1 Other : 6537 atoms
> > > 2 BUT : 84 atoms
> > > 3 CBD : 53 atoms
> > > 4 DEC : 6400 atoms
> > >
> > >
> > > On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <
> mark.j.abraham at gmail.com>
> > > wrote:
> > >
> > >> What does gmx make_ndx think?
> > >>
> > >> Mark
> > >>
> > >> On Thu, Jul 13, 2017 at 10:34 PM Alex <nedomacho at gmail.com> wrote:
> > >>
> > >> > Hi Mark,
> > >> > That's the problem: the names are exactly as they appear whenever
> atom
> > >> > group selections are made... Any thoughts?
> > >> > My topology is as clean as it gets:
> > >> >
> > >> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/
> forcefield.
> > >> itp"
> > >> > #include "but.itp"
> > >> > #include "cbd.itp"
> > >> > #include "decane.itp"
> > >> >
> > >> > [ system ]
> > >> > ; Name
> > >> >
> > >> >
> > >> > [ molecules ]
> > >> > ; Compound #mols
> > >> > BUT 7
> > >> > CBD 1
> > >> > DEC 200
> > >> >
> > >> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <
> > mark.j.abraham at gmail.com
> > >> >
> > >> > wrote:
> > >> >
> > >> > > Hi,
> > >> > >
> > >> > > As with any index group, you can make them with gmx make_ndx, gmx
> > >> select,
> > >> > > or your favourite text editor, and feed them to gmx grompp -n. You
> > >> > normally
> > >> > > get spoiled with automatically generated groups that happen to
> match
> > >> > > moleculetypes and such. So probably you have SOL already.
> > >> > >
> > >> > > Mark
> > >> > >
> > >> > > On Thu, Jul 13, 2017 at 9:55 PM Alex <nedomacho at gmail.com> wrote:
> > >> > >
> > >> > > > Hi all,
> > >> > > >
> > >> > > > I have a system that a subsystem of interest (molecules BUT and
> > CBD)
> > >> > and
> > >> > > > the solvent (DEC). I have simulated it and have a trajectory.
> > >> > > >
> > >> > > > I would like to find out the total energy of interaction between
> > BUT
> > >> > and
> > >> > > > CBD as a function of simulated time, so my thought is to do
> -rerun
> > >> and
> > >> > > > exclude the interactions in the following group pairs:
> > >> > > >
> > >> > > > DEC-DEC
> > >> > > > BUT-BUT
> > >> > > > CBD-CBD
> > >> > > > DEC-BUT
> > >> > > > DEC-CBD
> > >> > > >
> > >> > > > When setting energygrp-excl with the following pairs, I
> > immediately
> > >> > get a
> > >> > > > grompp error saying that DEC isn't an energy group. Since I've
> > never
> > >> > done
> > >> > > > this before, can you please share your wisdom?
> > >> > > >
> > >> > > > Thank you,
> > >> > > >
> > >> > > > Alex
> > >> > > > --
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